+Open data
-Basic information
Entry | Database: PDB / ID: 1j7o | ||||||
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Title | Solution structure of Calcium-calmodulin N-terminal domain | ||||||
Components | Calmodulin | ||||||
Keywords | METAL BINDING PROTEIN / EF hands / calcium binding / helix bundle / mini beta strand | ||||||
Function / homology | Function and homology information : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Chou, J.J. / Klee, C.B. / Bax, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains. Authors: Chou, J.J. / Li, S. / Klee, C.B. / Bax, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j7o.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7o.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7o ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8454.353 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): AR58 / References: UniProt: P62158, UniProt: P0DP23*PLUS |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: A total of five sets of dipolar couplings are measured, including the one-bond NH, CAHA, C'CA, and NC' couplings, and the two-bond C'HA couplings. Additionally, the sidechain CBHB dipolar ...Text: A total of five sets of dipolar couplings are measured, including the one-bond NH, CAHA, C'CA, and NC' couplings, and the two-bond C'HA couplings. Additionally, the sidechain CBHB dipolar couplings are measured to assign chi-1 rotamers for locked sidechains. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: This structure is determined mainly by residual dipolar couplings measured in A liquid crystalline Pf1 medium. The structure calculation scheme, described in the paper, is based on the idea ...Details: This structure is determined mainly by residual dipolar couplings measured in A liquid crystalline Pf1 medium. The structure calculation scheme, described in the paper, is based on the idea of refining existing structural models against dipolar couplings to derive thecorrect structure. Here a total of 323 backbone dipolar couplings are used to refine the backbone structure. Additionally, 38 sidechain dipolar couplings and 85 3-bond J couplings are used to determine the sidechain chi1 and chi2 rotamers as well as the presence of rotameric averaging. A total of three structures (model 1-3) were calculated starting from the 1. A crystal structure of Ca-calmodulin (PDB entry 1EXR), the NMR structure of apo-calmodulin (1F70), and the crystal structure of Ca-ligated parvalbumin (1CDP). The convergence of refinement is indicated by the small average RMSD between the three calculated structures and the average coordinates (0.28 A for backbone and 0.87 for all heavy atoms). During the three-stage simulated annealing described in the paper, restraints are included for most previously established hydrogen bonds, but have only minute effects (< 0.3 A) on the final structure. | ||||||||||||
NMR representative | Selection criteria: lowest dipolar energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structure with lowest dipolar energy Conformers calculated total number: 3 / Conformers submitted total number: 3 |